miRNA: 3'- cGCCGUGCCU----UGUGCUGGag---CAA-CGC- -5'
miRNA: 3'- -CGcCGUGCCUUG--UGCUGGa---GCAa--CGc -5'
miRNA: 3'- cGCCGUGCCUUG---UGCUGGAGCaaCGc -5'
miRNA: 3'- -CGCCGuGCCU------------UGUGCUGGaGCAACGc -5'
miRNA: 3'- -CGCCGUGCCUUGUGCUGGAGCAACGC- -5'
Results 21 - 25 of 25 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 27564 | 5' | -55.2 | NC_005882.1 | + | 26937 | 0.71 | 0.354146 |
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Target: 5'- uCGGCAUGGGgcggGCGCGGCCggcaaGUUcGCGg -3' miRNA: 3'- cGCCGUGCCU----UGUGCUGGag---CAA-CGC- -5' |
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| 27564 | 5' | -55.2 | NC_005882.1 | + | 26567 | 0.71 | 0.345619 |
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Target: 5'- cGCcGCGCGGAGCugGCGACCgucgCGUgggGCc -3' miRNA: 3'- -CGcCGUGCCUUG--UGCUGGa---GCAa--CGc -5' |
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| 27564 | 5' | -55.2 | NC_005882.1 | + | 18002 | 0.76 | 0.174761 |
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Target: 5'- aCGGUGCGGAACgucGCGACCUCGc-GCa -3' miRNA: 3'- cGCCGUGCCUUG---UGCUGGAGCaaCGc -5' |
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| 27564 | 5' | -55.2 | NC_005882.1 | + | 22877 | 0.78 | 0.121267 |
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Target: 5'- cGCGGC-CGGAugcgcgaguuuuGCACGGCC-CGUUGCc -3' miRNA: 3'- -CGCCGuGCCU------------UGUGCUGGaGCAACGc -5' |
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| 27564 | 5' | -55.2 | NC_005882.1 | + | 4959 | 1.1 | 0.000571 |
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Target: 5'- cGCGGCACGGAACACGACCUCGUUGCGc -3' miRNA: 3'- -CGCCGUGCCUUGUGCUGGAGCAACGC- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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